MultiGrain/MAPPER: A distributed multiscale computing approach to modelling and simulating gene regulation networks.

Alexandru Mizeranschi, Martin Swain, RALUCA SCONA, Quentin Fazilleau, Bartosz Bosak, Tomasz Piontek, Piotr Kopta, Paul Thompson, Dubitzky Werner

Research output: Contribution to journalArticle

3 Citations (Scopus)

Abstract

Modeling and simulation of gene-regulatory networks (GRNs) has become an important aspect of modern systems biology investigations into mechanisms underlying gene regulation. A key task in this area is the automated inference or reverse-engineering of dynamic mechanistic GRN models from gene expression time-course data. Besides a lack of suitable data (in particular multi-condition data from the same system), one of the key challenges of this task is the computational complexity involved. The more genes in the GRN system and the more parameters a GRN model has, the higher the computational load. The computational challenge is likely to increase substantially in the near future when we tackle larger GRN systems. The goal of this study was to develop a distributed computing framework and system for reverse-engineering of GRN models. We present the resulting software called MultiGrain/MAPPER. This software is based on a new architecture and tools supporting multiscale computing in a distributed computing environment. A key feature of MultiGrain/MAPPER is the realization of GRN reverse-engineering based on the underlying distributed computing framework and multi-swarm particle swarm optimization. We demonstrate some of the features of MultiGrain/MAPPER and evaluate its performance using both real and artificial gene expression data.
LanguageEnglish
Pages1-14
Number of pages14
JournalFUTURE GENERATION COMPUTER SYSTEMS-THE INTERNATIONAL JOURNAL OF GRID COMPUTING THEORY METHODS AND APPLICATIONS
Volume63
Early online date12 Apr 2016
DOIs
Publication statusPublished - 1 Oct 2016

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Distributed computer systems
Gene expression
Genes
Reverse engineering
Particle swarm optimization (PSO)
Computational complexity

Keywords

  • Gene-regulatory networks; Reverse-engineering of gene-regulation models; Distributed multiscale computing

Cite this

Mizeranschi, Alexandru ; Swain, Martin ; SCONA, RALUCA ; Fazilleau, Quentin ; Bosak, Bartosz ; Piontek, Tomasz ; Kopta, Piotr ; Thompson, Paul ; Werner, Dubitzky. / MultiGrain/MAPPER: A distributed multiscale computing approach to modelling and simulating gene regulation networks. In: FUTURE GENERATION COMPUTER SYSTEMS-THE INTERNATIONAL JOURNAL OF GRID COMPUTING THEORY METHODS AND APPLICATIONS. 2016 ; Vol. 63. pp. 1-14.
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MultiGrain/MAPPER: A distributed multiscale computing approach to modelling and simulating gene regulation networks. / Mizeranschi, Alexandru; Swain, Martin; SCONA, RALUCA ; Fazilleau, Quentin; Bosak, Bartosz ; Piontek, Tomasz ; Kopta, Piotr ; Thompson, Paul; Werner, Dubitzky.

In: FUTURE GENERATION COMPUTER SYSTEMS-THE INTERNATIONAL JOURNAL OF GRID COMPUTING THEORY METHODS AND APPLICATIONS, Vol. 63, 01.10.2016, p. 1-14.

Research output: Contribution to journalArticle

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AU - Swain, Martin

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AU - Bosak, Bartosz

AU - Piontek, Tomasz

AU - Kopta, Piotr

AU - Thompson, Paul

AU - Werner, Dubitzky

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